BIOL368/F11:Week 5

This journal entry is due on Wednesday, October 5 at midnight PDT(Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

You will then answer your research question from Week 4 using the bioinformatics tools you practiced with in Week 3.

You must create a multiple sequence alignment and tree using ClustalW.

You must also use one of the statistics you calculated, S, θ, or the Min and Max distances (or some other statistic mentioned in the Markham et al. (1998) paper.

Use your Web of Science prospective literature search results from the in-class activity to select a paper that was published within the last 5 years that studies the evolution of the env gene, in particular the V3 region, if possible. Include the bibilographic reference to this paper in your Week 5 journal.

Interpret your results in light of the data in this new paper.

You will prepare a presentation for Week 6 showing your results.

Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:

Title slide

Outline slide

Background that led you to ask your research question (summary of Markham et al. 1998)

Your question

How you answered your question, method/results

Interpretation of your results; answer to your question

Discussion and interprettion of your results in light of the new paper you found.

Upload your slides to the OpenWetware wiki by the Week 5 journal assignment deadline. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.

Furthermore, as alwasy, your electronic notebook should contain your notes, methods, results, and interpretations as you carry out your project. You should document as you work, taking your notes on the wiki as much as possible. Post data, figures, screenshots, to support your project. You can post files that are in progress; remember, you can upload a new version of the file and the wiki will automatically link to the new version (while keeping the old).

Although you will have assigned partner(s), you will need to fill out your own individual journal page with your own work.

Shared Journal Assignment

Store your journal entry in the shared BIOL368/F11:Class Journal Week 5 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )

Link to the shared journal entry from your user page.

Link the shared journal page to this assignment page.

Sign your portion of the journal with the standard wiki signature shortcut (~~~~).

Add the "BIOL368/F11" category to the end of the wiki page (if someone has not already done so).

Reflection

Answer these questions on the shared page:

What was the best part of working with a partner on this project? What was the worst part?

Besides the scientific conclusion of your project, what have you learned about the process of doing research as a result of this project?